In this video interview she discusses differential gene correlations to two different orthogonal gene expression measurements: a panel of over seven hundred TaqMan® genes, and whole-transcriptome RNA-Seq.

During the Advances in Genome Biology and Technology Conference Dr. Mark Andersen of Thermo Fisher R&D shared highlights of his presentation entitled “You want to put what where? Ion AmpliSeq™ technology, automation, any sample”. If you want to see what else the Ion Chef™ instrument can do, take a look!

At the Advances in Genome Biology and Technology Conference Dr. Adam Harris of Thermo Fisher Scientific R&D shared highlights of a presentation called “An avalanche of data: long reads and a speedy workflow with isothermal amplification”. How much time does this process save in template preparation? Watch and find out!

Here at Advances in Genome Biology and Technology there was a software bioinformatics demonstration session; we spoke with Dr. Carl Dowds Sr. Product Manager of Informatics Applications about the latest version of Ion Reporter™ Software and what it offers.

Studying genetic variation generally lays aside consideration for variants as they line up along a particular parental allele. While we accept that the human genome is diploid, in practice having two different forms of each allele is taken as individual homozygous or heterozygous single nucleotide variants at a given base position, rather than a string of variants lined up along distinct haploid genes.

Five years ago, Dr. Richard Gibbs of the Baylor College of Medicine gave a memorable plenary presentation at the annual Advances in Genome Biology and Technology conference in Marco Island, Florida."

Entitled “Genome Sequencing to Health and Biological Insight”, in his introduction he illustrated the seesaw battle between whole-genome or whole-exome sequencing approaches to a targeted sequencing approach by showing a drawing of two aluminum cans of popular cola soft-drinks, as a cartoon with boxing gloves. Illustrating this question of approaches as a battle, he said that while he favored the whole-genome / whole-exome sequencing approach he didn’t see any end to this struggle for the foreseeable future.

From clinical research, agricultural biotechnology, metagenomics, and technical improvements, here's a brief video roundup from yourteam at Behind the Bench of the major next-generation sequencing "moments that mattered" in 2014.

What would you do with free transcriptome sequencing? We asked that question in November 2014 during the Ion Torrent™ Transcriptome Profiling Grant Program. And over 200 researchers world-wide answered by submitting grant proposals for up to 24 samples of free sequencing using the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit, with sequencing services provided by our Certified Service Providers. Here are the winners...

While testicular cancer is relatively rare (about 8,500 cases in the US annually) it accounts for the most common solid tumor type in men aged 15 to 35. The vast majority (95%) are germ cell tumors, of which about half are called seminomas. These are usually slow growing and when discovered early are often treatable. The other half are called nonseminomas, are often more aggressive and can metastasize to other locations in the body.

Silicon Biosystems is a new company based in Italy that is developing a novel platform for solving the problem of heterogeneity of cells from tissues of many types. (For example, it is well-established that cancer is comprised of at least six cell types.) Their system uses microfabricated electrodes on a silicon chip married to a fluidic system, where a set of 9 electrodes form a di-electrophoretic ‘cage’ that enables single-cell trapping (as well as manipulation). These chips are called a DEPArray.

Nitrogen availability is one of the major limiting factors to crop growth. In the developed world where the use of nitrogen fertilizers are ubiquitous, their over-use causes nitrification of the environment and damaging algal blooms, in addition to atmospheric pollution. In the developing world, little access to fertilizers by smallholder farmers limits crop production, much more than the availability of water.

At the Plant and Animal Genome conference (held annually in San Diego California), many specialized sessions are devoted to specific crops and livestock. For example, on one afternoon there were 11 concurrent sessions, among which were Coffee Genomics, Curcurbit (otherwise known as pumpkins, squashes and gourds), and Domestication Genomics.

Circulating Tumor Cells (CTC) have rightly attracted a lot of interest in the field of cancer research, and in this interview Dr. Mitch Garcia discusses work that comes out of Dr. Hsian-Rong Tseng’s group at the University of California, Los Angeles.

new cases in the United States in 2014 alone. About 5% of these cases are inherited in an autosomal dominant fashion, and the two major types of these inherited cases are called familial adenomatous polyposis and hereditary non-polyposis colorectal cancer (HNPCC).

King Richard III had a short but notable reign (1483-1485), starting with the death of his brother, his 12-year old nephew Edward V declared an illegitimate heir to the throne, then Richard III ascending to the throne. His tumultuous reign ended when he was killed in battle by the forces of Henry VII. At the age of 32, he was the last of English Royalty to die in battle, and the only king whose remains were not known.

Kristian Ridley from Thermo Fisher Scientific shares what is new about genetic analysis from the exhibit floor of the recent Plant and Animal Genome Conference, along with observations about which products Thermo Fisher customers are interested in.

Speaking at the Plant and Animal Genome Conference, Dr. Jason Boone discusses Floragenics’ work on a variety of animal genomes in varied locales worldwide, as a genomics service provider. They have used genetics to track the pygmy elephant for conservation efforts, and also discusses the use of Ion AmpliSeq™ to perform rapid genotyping-by-sequencing with barley, and the cross-platform accuracy they’ve experimentally determined.

Don’t be paralyzed by too many choices for custom gene expression and genotyping assays

Having freedom to choose is a great thing. Having too many choices to choose from can be paralyzing. We have all been at a restaurant where the extensive menu meant that not only did it take a long time to make up your mind on what to have for dinner, but also it generated some concern that the optimal choice was not made. And then once the meal arrives for everyone at the table, this concern can likely turn into regret.

GeneSeek a genetic service provider, has been characterizing traits for agricultural biotechnology companies since 1998, with many capabilities across the genetic analysis spectrum including genotyping and SNP microarray technologies.

Cassava is a vitally important food crop worldwide. Otherwise known as manioc; in North America a well-known derivative form is tapioca. Native to northern Brazil, it spread throughout the South American continent and was carried by the Spanish and Portuguese explorers to the West Indies, then to the continents of Africa and Asia. Cultivated worldwide, an estimated 800 million people depend on it (500 million in Africa) as a main source of calories in their diet (up to 60%).

At the recent Plant and Animal Genome Conference, Monsanto computational biologist Dr. Lex Flagel discusses their work on the Western Corn Rootworm and the use of genotyping-by-sequencing to understand the genetic mechanism to Bt toxin resistance.

The International Rice Research Institute, located in Los Baños, Philippines, aims to reduce poverty and hunger, improve the health of rice farmers and consumers, and ensure environmental sustainability of rice farming.

James Schnable from the University of Nebraska-Lincoln has developed a technology called ‘tunable Genotyping by Sequencing’ (tGBS) that provides much better read-depth compared to conventional genotyping-by-sequencing approaches.

We are living in a remarkable, connected age – where all the world’s information is just a click away. It is hard to imagine that as few as twenty years ago to look up a publication abstract it meant going to an academic library and pull out the ISI Abstracts

reference volume(s). It seems quaint now, as looking up abstracts of journal articles are just a few clicks away.

You may be familiar with the Ion AmpliSeq™ Panels for highly multiplexed, single-tube PCR for next-generation sequencing target selection for human or mouse genes. You also may be familiar with the online AmpliSeq.com tool for making custom designs, as well as accessing gene lists and target coordinates for the standard research panels that are offered.

But did you realize that there are now several additional reference genomes to design a custom research panel from?

Dan Tonge has been working with the Ion Torrent™ platform for some time, and currently is working with uncultured fungi at very low concentrations. He discusses his approach toward how these amplicons are designed, and how they tested and challenged their ability to distinguish between closely related fungal species.

A huge neuroscience project is just getting started: will you be a part of it?

When you think of the largest government undertakings that had the largest impact in the modern era, what comes to mind? (By ‘impact’ you can consider the economic, social, or scientific ramifications excluding war, which of course is a separate question.)

A few talks and a workshop of interest at PAG XXIII January 10-14, 2015

The Plant and Animal Genome Conference calls itself ‘the largest Ag-Genomics meeting in the world’, and there is no reason to contest that. Do you work with arthropods like psyllids? There’s something for you. Aquaculture? There’s a day-long program devoted to it. Cacao? A whole afternoon set aside, now of particular importance given recent publicity around the growing worldwide chocolate deficit.

We’ve all grown accustomed to turning to YouTube to answer questions ranging from child care to yoga tips, or even how to deep fry a turkey. Back in 2012, we launched the Ask TaqMan video series with the belief that researchers are hungry for knowledge on a topic that’s very near and dear to our hearts: qPCR.

As it turns out, A LOT of people are in need of qPCR help, and in 2014 alone, the Ask TaqMan videos were viewed over 120,000 times! So what were those burning qPCR questions in 2014? Let’s take a look at the top 5 for the year…

Joel Dudley of the Icahn School of Medicine, The Mount Sinai Hospital (New York New York USA) discusses big data in the age of genomics. As a data scientist involved with the Resilience Project and its data-driven approach toward new discoveries with major research implications.

While I don’t know how you read your online newspaper or magazine, one great method of making sure you stay on top of important stories that can get lost in a sea of article titles is to scan the ‘Most Popular’ article list.

For 2014, these are the posts that were found to be most popular on Behind the Bench.

Searching for rare mutations in a majority wild-type background is a challenge when studying tumorigenesis. Earlier this year at the European Society for Human Genetics we interviewed a researcher using the QuantStudio® 3D Digital PCR System for rare KRAS mutations in cell-free DNA samples, and at that same meeting we also interviewed one of our internal application scientists who was looking at leukemia chimerism in a poster she presented.

Most embryos containing aneuploidy—an extra or loss of a chromosome—end up dying. However, some embryos containing this form of copy number variation do survive and develop to term. Some chromosomal aneuploidies that are viable end up forming the basis of diseases such as Down Syndrome (trisomy 21 or three chromosome 21 instead of the normal two), monosomy X (Turner Syndrome - just one X chromosome in females), Edwards syndrome (trisomy 18), Palau Syndrome (trisomy 13), -Klinefelter Syndrome (XXY, or two X chromosomes and a Y), and Triplo-X syndrome (XXX or three X chromosomes in females).

Looking at epigenetic marks using chromatin immunoprecipitation sequencing (ChIP-Seq), Dr. Brian O’Connor discusses his need to use as few as 1 million cells of flow-sorted cells identified by a particular cell subtype, and his work with Thermo Fisher Scientific staff scientists to develop a protocol for ChIP-Seq on the Ion Proton™ System.

Dr. Cardoso of the National Institute of Respiratory Diseases (Mexico City, Mexico) uses 16S rRNA sequencing to understand how the gut microbiome composition and its potential impact on HIV. She also discusses her use of the new Ion 16S™ Metagenomics Kit to classify the gut microbime composition and how the use of 7 variable regions compares to the single variable region she was using previously.

For years, researchers have been accustomed to running discrete executable programs (for example, on Microsoft Windows® operating systems) on attached computers that are purchased with a given instrument. Within the last few years, there has been a major shift toward storing email, photographs, and files online. The convenience of storing all this data online are manifold: the ability to access this information from multiple locations (whether a hotel lobby computer or a smartphone), the ability to share this information (for example, sharing holiday photographs with loved ones), and the convenience of not needing to maintain software updates and revisions along with migrating associated data.

Chris Mason (Weill Cornell Medical College, New York, New York USA) discusses his work with the recent ABRF study (Association for Biomolecular Research Facility) published recently in Nature Biotechnology.

He also discusses other projects he’s involved in, from metagenomic mapping in urban environments, as well as a multi-omics approach toward studying astronauts on the International Space Station.

How many times have you wished you could wave your magic wand at those degraded, low input samples and yell “Reparo”? You don’t have to be a fantasy-fiction aficionado to guess that “Reparo” is the charm that can be used to “repair” objects. Unfortunately, we live in a simple, non-magical world where the degradation of nucleic acids derived from FFPE blocks is a painful reality and we have to find innovative, “muggle” (i.e. non-magical) ways to work with it.

Dido Lenze discusses her experience adopting the Ion PGM™ System within a time-frame of only a few months, and her results comparing previously Sanger-sequenced samples with both the Ion AmpliSeq™ Colon and Lung Cancer Research Panel v2 and the Ion AmpliSeq™ Cancer Hotspot Panel v2.

She points out her use of known, difficult to detect deletions in control samples to challenge the NGS system, as well as some techniques they’ve developed to check the quality of their samples.

Joseph Boland (National Cancer Institute, Gaithersburg Maryland USA) using a prior technique and sequencing platform was able to only obtain 70% sequencing coverage. Find out how much better coverage they had in switching over to Ion Torrent sequencing for their research.

The human immune repertoire has a remarkable complexity of over 10^18 different T-cell receptors, and an even more diverse B-cell population. Recent interest in the Ion PGM System for immune repertoire sequencing has grown due to the extension of read-length to 400 bases, and the first publications are starting to appear.

The Life Technologies YouTube channel has hundreds of videos that cover just about everything in life sciences, from fundamental research to human identification to food safety. You can improve your qPCR with the Ask TaqMan or relive your glory days in the lab with Ph Diddy. What’s more impressive is that this massive library of videos received over 2.7 million views in this year alone! We pulled the data and listed the most popular videos in 2014 for your viewing pleasure. Sit back, relax, and enjoy your Thanksgiving downtime with these YouTube gems.

Daniela Starcevic (Icahn School of Medicine, The Mount Sinai Hospital, New York, NY USA) discusses her work with the Resilience Project and their development of a large Ion AmpliSeq™ Panel for targeted sequencing of hundreds of genes that cause rare disorders.

A growing area of research is using next-generation sequencing for sequencing the immune repertoire, which requires very long reads (400 base pairs and longer). Dr. Jiang Zhu of The Scripps Research Institute (La Jolla, California USA) developed very long reads using an Ion PGM TM System and a modified 5’-RACE technique.

At the recent International Society for Computational Biology, Latin America held in Belo Horizonte, Brazil, Dr. Victor Pylro of the Federal University of Vicosa gave a presentation called “Brazilian Microbiome Project: Revealing Unexplored Microbial Diversity – Challenges, Prospects and Standards”.

He made a strong case for the need for research on metagenomics in Brazil, as Brazil has about 20% of the world’s biological diversity, as well as the need for standardization of data analysis.

Using RNA sequencing for alleic differences (allele-specific expression) is an active area of research in further elucidating the role of variation to differences in phenotype.

Audrey Papp of The Ohio State University (Columbus Ohio USA) discusses her use of RNA-Seq to study allelic imbalances, and the new Ion AmpliSeq™ Transcriptome Human Gene Expression Kit to look at genome-wide gene expression from small tissue samples as well as from FFPE samples.

You probably have seen some of the online advertising about the Ion Torrent™ brand recently, featuring a ‘I am a #SeqWizard’ or ‘I am a #SampleSorcerer’ and making a statement such as “I get wider dynamic range and detect more genes than microarrays”. The following is this person’s interpretation of the ‘research personality type’ and some of the kinds of things he/her is known to think, say and behave in the lab.

In a recently published letter in the Annals of Hematology, Heinz Sill and collaborators at the Medical University of Graz, Austria report research on frequent mutations in the TP53 gene in archived neoplasm samples from treated subjects. The possibility they set out to explore is the presence of pre-existing mutations contributing to later leukemic transformation of hematopoietic stem cells in some individual samples.

In this brief video Dr. Andy Felton from Ion Torrent Product Management shares his thoughts with Jeremy Schoales during the Manchester stop on the Ion World Tour, and points out which presentations were highlights for him.

We’d say that both grant writing and FFPE (Formalin-Fixed, Paraffin-Embedded) blocks have a lot in common. Both are known to be notoriously difficult to deal with, and both have a certain aura of anxiety and trepidation associated with them. With the Ion Torrent™ Transcriptome Profiling Grant Program, we hope to drastically simplify both of these pain points. Talk about crossing two hurdles with a single leap!

In the last seven years that Chromatin Immunoprecipitation (ChIP) sequencing (ChIP-Seq) has been around, it has become the technique for showing us where transcription factor binding regions are found on chromosomes genome-wide. What’s important about that? Oh, just that these regions where proteins and DNA interact are essential to a number of biological processes like cell division and differentiation, gene regulation, nucleosome positioning, and epigenetic functions like histone and chromatin modification.

While looking over the past four days of presentations, poster sessions, social events and exhibitor interactions here are a few highlights and memorable moments at this year’s American Society for Human Genetics meeting.

Trujillano discusses his experience with comparing BRCA1/2 research samples previously sequenced by Sanger sequencing and the results he obtained on the Ion PGM™System with the Ion AmpliSeq™ Community Panels.

While phenotype-based bacterial classification has yet to be swept into history’s dustbin (the Gram stain is >130 years old this year!), an advancement, 16S rRNA sequencing, is making inroads to identifying bacteria for a range of applications.

Taking advantage of the evolutionary conservation of genes responsible for preparing mRNA for translation on the ribosome, 16S rRNA has the advantage of being small enough (1,542 nucleotide bases) to be easily cloned and sequenced.

To find out we spent some time with Dr. Jeffrey Ku, a scientist who works in Thermo Fisher Scientific’s Genetic, Medical and Applied Sciences Division. He’s a member of a group that interfaces with researchers and collaborates with them to develop new research applications.

Thousands packed the San Diego Convention Center this week to attend the 2014 American Society of Human Genetics annual meeting. But alas, countless others were not able to make the trip out sunny California. Not a problem – we have the next best thing: a guided tour of the Life Technologies booth and a run-down of all our activities at the meeting.

Daniel Rosenberg from the University of Connecticut has been studying the earliest stages of colorectal cancer using an experimental high-density colonoscopy technique. Here he discusses how the Arcturus®Laser Capture Microdissection System enables him to look at subtle changes in gene expression and gene sequence variation from very few cells.

After doing a genome-wide methylation scan in his reproductive biology research, Dr. Matthew Dyson of Northwestern University used theQuantStudio™ 3D Digital PCR System to quantify methylation status in a specific CpG island. He discusses the use of methylation-specific PCR (MSP) compared to a digital PCR-based solution.

Dr. Mike Lelivelt has written here about the improvements we’ve made in accuracy with the new Ion PGM Hi-Q™ Sequencing Kit. Now you can hear him this interview discussing the development of this kit and our future plans for expanding the use of this improved enzyme.

How can triple-negative breast cancer research samples be better characterized?

Milan Radovich of Indiana University discusses his work on this important cancer type using the new Ion AmpliSeq™ Transcriptome kit on the Ion Proton™ System, looking for expression-based gene signatures.

It is estimated that in the process of neural tissue differentiation that there may be greater than 100,000 possible neural cell types. Here is an interview with Dr. Yongming Sun of Thermo Fisher Scientific about their findings of new small RNA and gene expression markers from 15 different cell populations, including human embryonic stem cells and induced neural stem cells, and how RNA-Seq compares with current methods like immunocytochemistry.

Among several technologies on display at the American Society for Human Genetics annual conference, digital PCR certainly has garnered some buzz over the past couple of years. The small but mighty QuantStudio® 3D Digital PCR System made its public debut two years ago in San Francisco, and it has some great enhancements to boot this year in San Diego – specifically around rare mutation analysis.

Since being previewed at the European Society for Human Genetics annual meeting this summer, the Ion PGM™ Dx System has been making headlines lately. At the American Society for Human Genetics exhibit hall, we were able to grab some time with Peter Betzelos, leader of product management for diagnostics, to share some details about the system including its how it compares to the “Research Use Only” Ion PGM™ System and the rigorous process to develop a Dx platform.

One of the most important attributes for a DNA sequencing system is accuracy. Scientists want the highest quality, reproducible data. Sequencing systems have strengths and weaknesses driven by the unique chemistry of each. One criticism of the Ion Torrent™ sequencing chemistry has been that the fast and efficient lack of termination (which also gives it great speed) results in difficulty in long stretches of the same nucleotide (called a homopolymer tract). This results in a relatively high insertion and deletion (InDel) error rate.

Thermo Fisher Scientific collaborated with researchers at Stanford University (Palo Alto, California USA) and the Center for Geogenetics (Copenhagen, Denmark) to use the Ion Proton™ System to sequence ancient DNA extracted from tooth specimens at very low input (6ng – 39ng). These samples, from 1500 to 400 years BCE, were compared against two orthogonal sequencing technologies, and Dr. Jeff Ku from Thermo Fisher Scientific discusses these results.

Working with collaborators at National Jewish Health (Denver CO), Dr. Srinka Ghosh and other Applications Scientists at Thermo Fisher Scientific helped improve an existing ChIP-Seq protocol for the Ion Proton™ System, and presented their results in a poster titled “Approach for limited cell ChIP-Seq on a semiconductor-based sequencing system”.

We have blogged about the new AcroMetrix® Oncology Research Hotspot Control before, and now here is an interview with Thermo Fisher Scientific’s Dr. Nakul Nataraj on how this useful synthetic frequency control product was developed and verified.

Dr. Certa’s group is interested in pathway analysis during induced pluripotent stem cell differentiation. They use cardiomyocytes as a model, investigating what pathways are activated or deactivated upon drug candidate or compound administration. "In their compound testing process, slight changes in formulation may or may not affect toxicity and other important properties, and use gene expression as part of their development processes.

When researching retrospective cancer samples, a prime problem is the inherent heterogeneity of the starting material. Many experiments must be run in order to measure the performance of the system; in particular its sensitivity to pick up known mutations, whether single-nucleotide variants (SNVs), multiple nucleotide variants (MNVs), or insertions / deletions (what are called ‘indels’ collectively).

The concept of interrogating cell-free DNA from circulating plasma samples has gained popularity, and has been called a ‘liquid biopsy’. At Ion World Manchester, Dr. David Guttery and colleagues have been researching the use of the Ion PGM™ systemwith the Ion AmpliSeq™ Cancer Hotspot Panel V2 to detect low levels of circulating DNA.

Every year, thousands of geneticists worldwide converge for the annual American Society of Human Genetics meeting. This year it will be held in San Diego, California, from Saturday October 18 through Wednesday October 22. You can be sure there will be a flurry of activity, with interesting plenary talks, concurrent sessions (these concurrent sessions have no less than ten simultaneous sessions to choose from), educational sessions, exhibitor workshops, alumni receptions, and evening events.

Cate Faulkes from the Royal Surrey Hospital at the recent Ion World Tour in Manchester UK shares with us how the Ion Chef™ System save her laboratory time, and also some thoughts about using Ion Reporter™ software for research analysis.

At Ion World Manchester, Dr. Marcel Nelen from the Radboud University Medical Center Nijmegen shared how their group moved their routine research using Sanger sequencing over to the Ion PGM™ System. They took their existing primer designs for Sanger sequencing (including the M13-tailed primers), generated PCR amplicons, and then sheared them before performing a standard DNA library preparation.

Mutational profiling for Acute Myeloid Leukemia (AML) has been performed for over a decade, as most AML samples are found to be cytogenetically normal. However in absence of being able to create immortal cell lines or mouse xenografts, genetic changes that need to be detected have to be performed with a background of normal cells (a heterogeneous cell population). Due to these factors, as well as the availability of samples with a minimum on non-cancerous cell background, AML was the first cancer genome to be sequenced in 2008.